Oblique collision between the Caribbean plate and the Bahama Banks has lead an eastward migration of the northern Caribbean plate boundary by successive southward jumps of major strike-slip faults. The Septentrional-Oriente Fault zone (SOFZ) defines the present-day northern Caribbean plate boundary accommodating most of the eastward escape of the Caribbean plate. Here, we reevaluate the complex history of the SOFZ along the Windward Passage area between the easternmost region of Cuba and the northwest of Haiti. Based on seismic reflection and swath-bathymetric data set we interpret the structure and tectonic pattern of the Windward Passage. The tectono-sedimentary framework of this large strait shows contrasting patterns of deformation linked to a complex polyphase tectonic history of dominantly strike-slip faulting. SOFZ segments offset the seismic units and yield key markers of displacement along the fault system. Our study provides structural and stratigraphic insights into the relative timing of deformation along the Windward Passage and presents new elements that constrain the southeastward jump of the north Caribbean plate boundary to its present-day position. We propose dates for the identified seismic units based on the correlation of offshore deformation phases recorded in the Windward Passage sedimentary cover with major paleogeographic reorganization episodes described onland (Late Eocene, Late Oligocene, Middle Miocene and Late Pliocene). By restoring the offset of the seismic units, we demonstrate that at least ∼80 km of left-lateral motion has occurred on the SOFZ, and that the SOFZ has been active since the Pliocene.